The first archeological site documented in West Virginia was eight figures from the Brown's Island Petroglyph (46HK8). Benjamin S. Barton visited the site ca. 1785 and published the figures in 1799

The first archeological excavation undertaken in West Virginia was at Grave Creek Mound at Moundsville in 1838. In the fall of 1846, when Ephraim G. Squier and Edwin H. Davis documented the Salt Rock petroglyphs along the Guyandotte River in Cabell County. Their report, published in 1848, was included in the first volume of the Smithsonian Institution's "Contributions to Knowledge" series, titled Ancient Monuments of the Mississippi Valley.

The early settlers believed a prehistoric race of people they called "Mound Builders" constructed the burial mounds and earthworks. The Mound Builders were viewed as an ancient race from Europe, Africa, or the Near East, who had vanished and been replaced by American Indians. Some early scholars believed the Mound Builders were one of the Lost Tribes of Israel.

In 1881, Congress gave $5,000 to the Smithsonian Institution to conduct archeological excavations relating to the prehistoric Mound Builders. Wills De Hass of Wheeling was put in charge of the project. He was replaced by Cyrus Thomas after one year. Col. P. W. Norris led the mound explorations for the Smithsonian in the Kanawha Valley from 1882 to 1884. Norris dug a deep shaft into the Criel Mound in South Charleston, the second-largest mound in West Virginia, and found an individual buried with a copper headdress, six shell beads, and one flint knife.

The goal of the Smithsonian mound explorations was to settle the question of the identity of the Mound Builders. By 1890, more than 2,000 mounds and earthworks had been studied in the eastern United States. About 100 of these were in the Kanawha Valley. In 1894, Cyrus Thomas published Report on the Mound Explorations of the Bureau of Ethnology and proved the Mound Builders were not a vanished race but ancestors of American Indians. This publication marks the birth of modern American archeology.

During the late 1800s the Smithsonian continued to be active in West Virginia. Gerard Fowke published on numerous archeological sites in the eastern region and on artifacts in the Kanawha Valley. John P. MacLean investigated several sites on Blennerhassett Island, and Garrick Mallery described a pictograph and several petroglyph sites in West Virginia. During the early 1900s most of the published references to archeological sites came from county histories.

The 1930s saw the beginning of university involvement, reflecting the growth of the new field of descriptive anthropology. Charles Bache and Linton Satterwaite Jr., of the University of Pennsylvania, excavated the Beech Bottom Mound in Brooke County and published their findings in the Museum Journal in 1930. James B. Griffin visited several village sites and defined the Clover Phase in 1943.

After World War II, a group of amateur archeologists began working with Dr. Ralph Solecki and the Smithsonian Institution's River Basin Survey on the Bluestone Reservoir project. In 1949, Robert and William Athey, Joseph Essington, Elmer W. Fetzer, Oscar L. Mairs, and Delf Norona joined with Solecki and founded the West Virginia Archeological Society. In the same year they began publication of the West Virginia Archeologist.

By 1950, Sigfus Olafson, a Boone County geologist, began publishing articles on petroglyphs, the painted trees, Gabriel Arthur, and other subjects. West Virginia joined the Eastern States Archeological Federation, and Olafson eventually became president of both organizations.

While members of the Archeological Society were active in documenting and interpreting West Virginia's prehistory, they recruited professional archeologists James Kellar, Ralph Solecki, and Frank Setzler to conduct major investigations and excavations at Mount Carbon Stone Walls, Natrium Mound, and Welcome Mound. During the 1950s the Carnegie Museum at Pittsburgh began its Upper Ohio Valley Archeological Survey, with extensive fieldwork conducted in northern West Virginia by William J. Mayer-Oakes and Don Dragoo. Many classic sites were excavated, including the Speidel Site, Watson Farm, Globe Hill, Cresap Mound, Dixon Rock Shelter, and Rohr Rock Shelter.

The West Virginia Archeological Society with the assistance of Dr. Paul H. Price, the state geologist, convinced the state legislature in 1960 to create the position of state archeologist. Dr. Edward V. McMichael was hired, and the West Virginia Geological and Economic Survey's Section of Archeology was created.

The 1960s were the golden years of West Virginia archeology. McMichael conducted major excavations at the Buffalo Site and Mount Carbon and with the assistance of society members conducted archeological surveys and test excavations throughout the state. Bettye J. Broyles received National Science Foundation grants to excavate at the St. Albans Site. The Section of Archeology began its own publication series and continued to publish extensively in the West Virginia Archeologist. By 1968, McMichael had published his Introduction to West Virginia Archeology, which continues to be the only major overview of West Virginia archeology. By 1970, McMichael had left the Geological Survey. Broyles replaced him and was eventually replaced by Daniel B. Fowler.

In 1965 the West Virginia Antiquities Commission was established, and archeology was included in its program. In 1966, Congress enacted the National Historic Preservation Act, which established the National Register of Historic Places, requiring each state to appoint a state historic preservation officer and a board to review grants. The Antiquities Commission assumed these responsibilities in West Virginia.

After the passage of the Moss-Bennett Bill in 1974 federal agencies had to comply with the National Historic Preservation Act, and cultural resources management became the dominating force in West Virginia archeology. Cultural resources management, the practice of managing archeological and historic sites, involves excavating, analyzing, stabilizing, and documenting sites and structures that are endangered. Federal agencies responded to the new legislation by hiring professional archeologists and integrating cultural resources management into the federal planning process.

On July 1, 1977, the West Virginia Antiquities Commission was supplanted by the Archives and History Commission at the newly created West Virginia Department of Culture and History. The new department consolidated West Virginia's arts and history programs. Gradually, much of the responsibility for archeology was transferred to the historic preservation office at Culture and History. The West Virginia Geological and Economic Survey phased out its archeology program. Daniel B. Fowler, who served as state archeologist with the Geological and Economic Survey, moved to the Blennerhassett Historical Park Commission on May 21, 1979, and the survey's archeological collections were moved to Blennerhassett Museum in March 1984. The 1,600 boxes of artifacts and 73 boxes of associated documents were moved to the Delf Norona Museum in Moundsville on October 1, 1996.

During the 1980s and 1990s most professional archeological work in West Virginia was accomplished under federally funded cultural resources management projects, usually by out-of-state consulting firms. Professional archeologists working in West Virginia banded together to form the Council For West Virginia Archaeology, incorporated on October 8, 1985. Its members have earned at least a master's degree or equivalent and work in archeology or related fields.

In 1990, Congress passed the Native American Graves Protection and Repatriation Act, which had a major impact on American archeology. West Virginia has no federally recognized Native American tribes or Indian reservations, and none of the prehistoric skeletal remains recovered in the state can be associated with historic tribes. On September 14, 1990, the state historic preservation officer, William Drennen, entered into a memorandum of understanding with the West Virginia Committee on Native American Archaeological and Burial Policies which led to the Cotiga Mound Memorandum of Agreement. This agreement essentially gave the Native American Committee control over the Department of Highways excavation of an Indian burial mound in Mingo County. After several meetings the West Virginia Archeological Society, the Council For West Virginia Archaeology, and the United Cherokee Tribe of West Virginia filed a lawsuit against the state to rescind the agreement. The West Virginia Department of Transportation and the State Historic Preservation Office prevailed in the case, but the Cotiga excavations were opened to the public and many of the stipulations were reinterpreted to the benefit of archeologists.

While West Virginia University and Marshall University have archeology classes, there is no strong university program in prehistoric or historic archeology. The West Virginia University Institute for the History of Technology and Industrial Archaeology, founded by Dr. Emory Kemp, provides the state with an excellent program in industrial archeology.

As of May 2021, West Virginia had 16,688 recorded archeological sites and the number continues to increase. The number of in-state cultural resources management firms continues to grow, and there is a dramatic increase in highway archeology. More accurate cultural chronologies are being developed based on 450 radiocarbon dates for West Virginia and state of the art analysis techniques. Continued collaboration between the state's archeological organizations will ensure the future of West Virginia archeology.